Chlamydia Research Today is a free monthly online journal that collates and summarizes the latest research about Chlamydia, including details on symptoms, diagnosis, treatment, causes, problems.

In silico prediction and functional validation of sigma28-regulated genes in Chlamydia and Escherichia coli.

Yu HH, Kibler D, Tan M

Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697-4025, USA.

sigma(28) RNA polymerase is an alternative RNA polymerase that has been proposed to have a role in late developmental gene regulation in Chlamydia, but only a single target gene has been identified. To discover additional sigma(28)-dependent genes in the Chlamydia trachomatis genome, we applied bioinformatic methods using a probability weight matrix based on known sigma(28) promoters in other bacteria and a second matrix based on a functional analysis of the sigma(28) promoter. We tested 16 candidate sigma(28) promoters predicted with these algorithms and found that 5 were active in a chlamydial sigma(28) in vitro transcription assay. hctB, the known sigma(28)-regulated gene, is only expressed late in the chlamydial developmental cycle only, and two of the newly identified sigma(28) target genes (tsp and tlyC_1) also have late expression profiles, providing support for sigma(28) as a regulator of late gene expression. One of the other novel sigma(28)-regulated genes is dnaK, a known heat shock-responsive gene, suggesting that sigma(28) RNA polymerase may be involved in the response to cellular stress. Our sigma(28) prediction algorithm can be applied to other bacteria, and by performing a similar analysis on the Escherichia coli genome, we have predicted and functionally identified five previously unknown sigma(28)-regulated genes in E. coli.

Published 19 November 2006 in J Bacteriol, 188(23): 8206-12.
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